[x] On the front page README.md when describing the deletions for the different variants, how about H69- instead of H69 ?
[x] Can we update the visualization of the superfolder-v2's on the front page README.md to show the Delta variant superfolders (both the hotfix and the new one from Eterna)?
[x] OpenVaccine consortium, 2021, in prep --> update ref. to bioRxiv.
[x] The sequence was designed based on simulations with standard nucleosides A, C, G, and U. --> put in a note about PSU, and perhaps link to the challenge on Eterna.
On analysis.md:
[x] In the table, need to convey that half-life is in hours (maybe in footnote), and give the 'stress' conditions under which we calibrated the relationship of DegScore to half-life.
[x] Can we point folks to an explanation and plot of that calibration of DegScore to half-life?
[x] For me, the footnotes in the table are one after the other -- would beeasier to read with linebreaks.
[x] The Superfolder construct was optimized by Eterna participants to reduce predicted degradation. -- is that Superfolder-v2?
[ ] The Superfolder-Delta construct was developed by enumerating all GC-rich codon substitutions to result in the Delta mutant spike protein, evaluating their DegScore, and selecting the variant with the lowest DegScore. --> want to point folks who want to reproduce this analysis to mRNA-hotfix entry on eternagame.stanford.edu/about/software
[x] Need to explain Superfolder-Delta-PSU
[x] Its unclear in bargraph what Superfolder refers to. Can the order of entries in the bargraph be preserved compared to the table?
[x] In December 2021, --> In December 2020,
[ ] Can we show a ribographviz gallery of the Superfolder-Delta-PSU designs?
I like superfolders_ALL.csv
[x] Can we add a column that specifies the sequence it was designed for? Either S-2P or S-2P, B.1.617.2 (any rows with S-2P, B.1.617)?
[x] Why do pfizer-Delta-hotfix and moderna-Delta-hotfix appear twice?
Some tiny suggestions --
README.mdwhen describing the deletions for the different variants, how aboutH69-instead ofH69?README.mdto show the Delta variant superfolders (both the hotfix and the new one from Eterna)?OpenVaccine consortium, 2021, in prep--> update ref. to bioRxiv.The sequence was designed based on simulations with standard nucleosides A, C, G, and U.--> put in a note about PSU, and perhaps link to the challenge on Eterna.On
analysis.md:The Superfolder construct was optimized by Eterna participants to reduce predicted degradation.-- is that Superfolder-v2?The Superfolder-Delta construct was developed by enumerating all GC-rich codon substitutions to result in the Delta mutant spike protein, evaluating their DegScore, and selecting the variant with the lowest DegScore.--> want to point folks who want to reproduce this analysis tomRNA-hotfixentry on eternagame.stanford.edu/about/softwareSuperfolder-Delta-PSUSuperfolderrefers to. Can the order of entries in the bargraph be preserved compared to the table?I like
superfolders_ALL.csvS-2PorS-2P, B.1.617.2(any rows withS-2P, B.1.617)?pfizer-Delta-hotfixandmoderna-Delta-hotfixappear twice?